OMOP2OBO

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TODO - Pubs+Presentation Task: Deposit versions in Zenodo to get citable DOI

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Deposit versions in Zenodo to get citable DOI

jmcmurry

Harmonise OMOP mappings with boomer or a boomer-like approach?

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Currently, the mappings generated by omop2obo do not respect the semantic constraints of all participating ontologies (which makes some sense because of the significant negative impact on performance). For example,...

matentzn

Coding: SSSOM Output

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## Basic description Feature request. Allow option for mappings outputs to be in SSSOM format. **Action:** Generate mapping outputs. **Output:** Rather than the existing output format, this would output mappings...

joeflack4

test_string_similarity failed for me because the nltk download isn't working. I found a way to get the download to work here: https://stackoverflow.com/questions/38916452/nltk-download-ssl-certificate-verify-failed After failing to get the solutions that fix...

chrisroederucdenver

fix #65 no value for merge option does not issue error about multiple…

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Now it shows a friendlier message "Error: Missing option '--clinical_domain'."

chrisroederucdenver

fixes #68

chrisroederucdenver

**Describe the bug** running without a mrconso file creates an error **To Reproduce** Steps to reproduce the behavior: (test_env) CARD-CRoeder:OMOP2OBO christopherroeder$ time ./main.py --clinical_domain condition --clinical_data resources/clinical_data/sample_conditions.csv **Expected behavior** no...

chrisroederucdenver

for issue #63

chrisroederucdenver

merge option fails with multiple

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**Describe the bug** If you run with no arguments (as you very likely would not) you get: "ValueError: 'default' must be a list when 'multiple' is true." **To Reproduce** Steps...

chrisroederucdenver

Coding: add requirements.txt

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Add a requirements.txt to make it easier to create an environment with required libs.

chrisroederucdenver